Just looked at the reference material that downloads with the 1.0.5 IDE trying to find out if the hardware Serial also supports the inverse_logic flag in the Serial.begin (or any other command) like SoftwareSerial does and I notice it's so out of date it does not even mention you can specify the protocol (8N1, 7O2 etc) after the baud rate that has been present online for months now.
Why are the local reference files so out of date? And can/how do I specify inverse logic for serial data?
HardwareSerial does NOT support inverse logic. You'll have to add an external (hardware) inverter.